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EC and GECKO Models

pipeGEM includes enzyme-constrained integration helpers under pipeGEM.integration.ec.

The public entry points are:

  • apply_gecko_light
  • apply_gecko_full
  • auto_parameterize

Use these workflows when reaction capacity should be constrained by enzyme usage, molecular weight, kcat, or automated parameterization data.

from pipeGEM.integration.ec import apply_gecko_light

ec_model = apply_gecko_light(model)

GECKO and enzyme-constrained workflows depend on enzyme metadata quality. Check reaction-gene mappings, enzyme molecular weights, kcat coverage, and units before interpreting flux differences.